Understanding shared variation in SARS-CoV-2 genomes

The project is a collaborative effort of investigators from the University
of California, Berkeley’s Innovative Genomics Institute (IGI) and School
of Public Health (SPH); Kaiser Permanente Northern California (KPNC); and
the California Department of Public Health (CDPH), with administrative and
programmatic support provided by Heluna Health. Over the project period,
the collaborating investigators will analyze approximately 35,000 genomes
of SARS-CoV-2 specimens obtained from KPNC members and sequenced by the
CDPH through its COVIDNet activities. By combining results from the
genomic analysis of low-frequency alleles with clinical and epidemiologic
data available in patient records, including demographic variables,
COVID-19 vaccination status (dates of vaccination; number of doses;
manufacturer), COVID-19 disease severity, and underlying medical
conditions, we assessed which shared genomic variations are associated
with a greater risk of symptomatic infection and severe clinical outcomes;
COVID-19 vaccine effectiveness; and transmission of SARS-CoV-2 in the
household. The project and its results can serve as a model for
community-based monitoring of the evolution and spread of SARS-CoV-2 and
use of the data to inform decisions about the formulation and use of
COVID-19 vaccines, including booster doses and next-generation vaccines.